It's based on the plug-in I made for Total Commander, but you can also use other programs allowing you to transfer files to the iPod via USB, and allowing you to rename iPod files (not sure any of them can, as of today, I didn't try).

Next thing you want to do is install MobileFinder on your iPod, it will allow you to change the permissions of files. USB transfers reset the executable flags of applications (Apple only meant that to transfer media files, not apps), so MobileFinder can be used to restore them on the iPod.Download MobileFinder. You can get the application with this command, but I've put the file in attachment for those who don't have wget:
wget -U "AppTapp Installer/3.0b8 (iPhone)" http://ste-pkg.org/iphone-apps/zips/mobilefinder-1.8.0.zip

Unzip the file, it will create a Mobile.app directory in your download directory on your PC.
For the sake of this guide, let's say you unzipped it to C:\Temp\Finder.app. So under C:\Temp\Finder.app, you should see all the application files and png images.

Launch Total Commander, and browse to your iPod application directory in the left panel, and to your C:\Temp directory in the right panel:

Press TAB to switch to the left panel, move down to select the Finder.app directory, and press Ctrl Right key to open this directory in the right panel (you can also go to this directory from the right panel directly, it's just a shortcut):

Attached Files:

Enter the Calculator directory in the left panel, and move (F6 key) the Calculator file to the right panel. Don't copy it, move the file, it's important.
TAB to go to the right panel, delete the Finder file.
Rename Calculator to Finder, with Shift-F6:

Go back to the C:\Temp directory in the right panel: you can use Alt Left key, or simply select the C drive (Alt F2 or the drive drop-down box).
Copy Calculator back to the left panel.Note: now Calculator won't have the execute flag set, since it's copied from the PC. We'll have to put it back later with Finder. A small but necessary sacrifice

Note: The Finder on the left has the wrong size because it's the Calculator app we renamed earlier.

As you would guess, copy the right Finder file into the left directory and confirm the overwrite.

Note: copying onto an existing file preserves the permissions!

Congrats, you're done! Now you can reboot your iPod to see the new application. If you have SysInfo or SummerBoard you can simply restart SpringBoard, otherwise switch the iPod off, then on again.

You should have the Finder application now. Don't forget to use it to set the execute permission back to the err, wonderful Calculator app:

Start Finder, wait a few seconds until it has initialized.

Tap on Settings, switch off the Application Launch option. Go Back to the application.

Tap on the apple symbol (top right). You will see the following folders: Applications, Bookmarks, Sync, Trash.

Tap twice on Applications, then twice on Calculator.app. You will be in the calculator application directory.

Scroll down to the Calculator file, tap once on it to highlight the file, and tap on Modify at the bottom.

Tap on the Owner Exec flag to make it change to the blue colour (it can be a little tricky sometimes). Tap on Done.

You can exit the application with the Home button and check if your calculator is working.

Now you're ready to install other applications manually. Be careful, some applications (like SummerBoard) require more than simply copying files from the PC to the /Applications directory, you might need to edit files from the iPod... but most of them are quite easy to install.

Basically, you'll have to set the Exec flags of the applications, like you just did for the calculator. There might be serveral executable files in some applications, but this is out of the topic of this little guide.

No, but I haven't looked, for now I've been mainly using Wi-Fi to install applications. If you want to see how to install an application manually, for example one from http://repository.apptapp.com, read the repository script with this command:

I'm using Cygwin which is a Linux-like environment in Windows (you have the same shell, the GNU tools and so on... and wget), I suppose that wget exists on MacOS too. But if you have neither of that, a little program doing the same is easy to write, I can post one if you want.

EDIT: made one anyway, I needed to test something and it was just one click away

And with a little getting used to, you see that the name of the application follows the "name" key tag, that the .zip file follows the "location" key tag, and so on. You can download the zip file as before with:

That being said, I'm currently developing a Windows application that checks repositories, builds a package with the applications you want to install/update, and stores it on the iPod. Then an iPod application will install the package contents. So the wireless won't be necessary anymore except to install this first "USB installer" on the iPod (and then again, it's possible to install it without Wi-Fi with the method above). With the advantage that you won't have to endure the endless refresh of the current Installer, have a better bandwidth, and that you will be able to get a history of the versions on your PC (among other things).

It just leaves the jailbreak part. Plus everytime you'll have to restore if this app contains enough bug to render the iPod useless